Related papers: A new distance for high level RNA secondary struct…
In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Gro\ss e-Rhode's Algebra Transformation Systems.
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
In many applications, it is necessary to determine the string similarity. Edit distance[WF74] approach is a classic method to determine Field Similarity. A well known dynamic programming algorithm [GUS97] is used to calculate edit distance…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
Many neural network pruning algorithms proceed in three steps: train the network to completion, remove unwanted structure to compress the network, and retrain the remaining structure to recover lost accuracy. The standard retraining…
Between the leaves and the nodes of a complete binary tree, a separate parent-child-sister hierarchy is employed independent of the parent-child-sister hierarchy used for the rest of the tree. Two different versions of such a local…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Scope of reproducibility: We are reproducing Comparing Rewinding and Fine-tuning in Neural Networks from arXiv:2003.02389. In this work the authors compare three different approaches to retraining neural networks after pruning: 1)…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
Recurrent neural networks (RNNs) have recently achieved remarkable successes in a number of applications. However, the huge sizes and computational burden of these models make it difficult for their deployment on edge devices. A practically…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
Given an ensemble of randomized regression trees, it is possible to restructure them as a collection of multilayered neural networks with particular connection weights. Following this principle, we reformulate the random forest method of…
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Graph edit distance (GED) is a powerful and flexible graph matching paradigm that can be used to address different tasks in structural pattern recognition, machine learning, and data mining. In this paper, some new binary linear programming…